10 20 30 40 50 60 70 80 153D - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric Unit
HEADER DNA 16-DEC-93 153D
TITLE CRYSTAL STRUCTURE OF A MISPAIRED DODECAMER, TITLE 2 D(CGAGAATTC(O6ME)GCG)2, CONTAINING A CARCINOGENIC O6- TITLE 3 METHYLGUANINE
COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA (5'-D(*CP*GP*AP*GP*AP*AP*TP*TP*CP*(6OG) COMPND 3 P*CP*G)-3'); COMPND 4 CHAIN: A, B; COMPND 5 ENGINEERED: YES
SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES
KEYWDS B-DNA, DOUBLE HELIX, MODIFIED, MISMATCHED
EXPDTA X-RAY DIFFRACTION
AUTHOR S.L.GINELL,J.VOJTECHOVSKY,B.GAFFNEY,R.JONES,H.M.BERMAN
REVDAT 2 24-FEB-09 153D 1 VERSN REVDAT 1 15-JAN-94 153D 0
JRNL AUTH S.L.GINELL,J.VOJTECHOVSKY,B.GAFFNEY,R.JONES, JRNL AUTH 2 H.M.BERMAN JRNL TITL CRYSTAL STRUCTURE OF A MISPAIRED DODECAMER, JRNL TITL 2 D(CGAGAATTC(O6ME)GCG)2, CONTAINING A CARCINOGENIC JRNL TITL 3 O6-METHYLGUANINE JRNL REF BIOCHEMISTRY V. 33 3487 1994 JRNL REFN ISSN 0006-2960 JRNL PMID 8142345 JRNL DOI 10.1021/BI00178A004
REMARK 1
REMARK 2 REMARK 2 RESOLUTION. 2.90 ANGSTROMS.
REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : NUCLSQ REMARK 3 AUTHORS : WESTHOF,DUMAS,MORAS REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 8.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 2.000 REMARK 3 COMPLETENESS FOR RANGE (%) : NULL REMARK 3 NUMBER OF REFLECTIONS : 1031 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 R VALUE (WORKING + TEST SET) : 0.169 REMARK 3 R VALUE (WORKING SET) : NULL REMARK 3 FREE R VALUE : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : NULL REMARK 3 REMARK 3 FIT/AGREEMENT OF MODEL WITH ALL DATA. REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : NULL REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : NULL REMARK 3 FREE R VALUE (NO CUTOFF) : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : NULL REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : NULL REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 0 REMARK 3 NUCLEIC ACID ATOMS : 490 REMARK 3 HETEROGEN ATOMS : 2 REMARK 3 SOLVENT ATOMS : 49 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM SIGMAA (A) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 DISTANCE RESTRAINTS. RMS SIGMA REMARK 3 SUGAR-BASE BOND DISTANCE (A) : 0.012 ; 0.020 REMARK 3 SUGAR-BASE BOND ANGLE DISTANCE (A) : 0.022 ; 0.025 REMARK 3 PHOSPHATE BONDS DISTANCE (A) : 0.023 ; 0.025 REMARK 3 PHOSPHATE BOND ANGLE, H-BOND (A) : 0.024 ; 0.025 REMARK 3 REMARK 3 PLANE RESTRAINT (A) : 0.012 ; 0.020 REMARK 3 CHIRAL-CENTER RESTRAINT (A**3) : 0.090 ; 0.100 REMARK 3 REMARK 3 NON-BONDED CONTACT RESTRAINTS. REMARK 3 SINGLE TORSION CONTACT (A) : 0.130 ; 0.300 REMARK 3 MULTIPLE TORSION CONTACT (A) : 0.180 ; 0.300 REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 SUGAR-BASE BONDS (A**2) : 0.530 ; 2.000 REMARK 3 SUGAR-BASE ANGLES (A**2) : 0.790 ; 2.000 REMARK 3 PHOSPHATE BONDS (A**2) : 3.630 ; 4.000 REMARK 3 PHOSPHATE BOND ANGLE, H-BOND (A**2) : 2.630 ; 8.000 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL
REMARK 4 REMARK 4 153D COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL.
REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 133.00 REMARK 200 PH : 7.00 REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : ENRAF-NONIUS FR571 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : NULL REMARK 200 WAVELENGTH OR RANGE (A) : NULL REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : DIFFRACTOMETER REMARK 200 DETECTOR MANUFACTURER : ENRAF-NONIUS CAD4 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 2924 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.300 REMARK 200 RESOLUTION RANGE LOW (A) : NULL REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : NULL REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: NULL REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL
REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): NULL REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): NULL REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PH 7.00, VAPOR DIFFUSION, REMARK 280 TEMPERATURE 277.00K
REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 12.56500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 32.25500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 20.22500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 32.25500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 12.56500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 20.22500 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL
REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA.
REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000
REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 DC B 13 O3' DG B 14 P -0.086 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 DC A 1 O5' - C5' - C4' ANGL. DEV. = -7.9 DEGREES REMARK 500 DC A 1 C4' - C3' - C2' ANGL. DEV. = -4.6 DEGREES REMARK 500 DC A 1 C3' - C2' - C1' ANGL. DEV. = -6.9 DEGREES REMARK 500 DC A 1 O4' - C1' - N1 ANGL. DEV. = 5.2 DEGREES REMARK 500 DG A 2 C1' - O4' - C4' ANGL. DEV. = -9.1 DEGREES REMARK 500 DG A 2 O4' - C1' - N9 ANGL. DEV. = 3.0 DEGREES REMARK 500 DG A 2 C5 - C6 - N1 ANGL. DEV. = 3.3 DEGREES REMARK 500 DA A 3 O4' - C1' - C2' ANGL. DEV. = -5.4 DEGREES REMARK 500 DA A 3 C6 - N1 - C2 ANGL. DEV. = 3.6 DEGREES REMARK 500 DA A 3 N1 - C2 - N3 ANGL. DEV. = -3.2 DEGREES REMARK 500 DG A 4 O5' - P - OP1 ANGL. DEV. = 7.2 DEGREES REMARK 500 DG A 4 O4' - C1' - N9 ANGL. DEV. = 2.2 DEGREES REMARK 500 DG A 4 C5 - C6 - N1 ANGL. DEV. = 3.0 DEGREES REMARK 500 DA A 5 N1 - C2 - N3 ANGL. DEV. = -3.1 DEGREES REMARK 500 DA A 6 O5' - C5' - C4' ANGL. DEV. = -5.0 DEGREES REMARK 500 DT A 7 O5' - C5' - C4' ANGL. DEV. = -5.0 DEGREES REMARK 500 DT A 7 C2 - N3 - C4 ANGL. DEV. = -5.1 DEGREES REMARK 500 DT A 7 N3 - C4 - C5 ANGL. DEV. = 4.3 DEGREES REMARK 500 DA A 6 C3' - O3' - P ANGL. DEV. = 10.5 DEGREES REMARK 500 DT A 8 O4' - C1' - N1 ANGL. DEV. = 2.1 DEGREES REMARK 500 DT A 8 C2 - N3 - C4 ANGL. DEV. = -4.3 DEGREES REMARK 500 DT A 7 C3' - O3' - P ANGL. DEV. = 8.2 DEGREES REMARK 500 DC A 9 N3 - C4 - C5 ANGL. DEV. = -2.7 DEGREES REMARK 500 DT A 8 C3' - O3' - P ANGL. DEV. = 8.6 DEGREES REMARK 500 DC A 11 P - O5' - C5' ANGL. DEV. = -13.6 DEGREES REMARK 500 DG A 12 O4' - C1' - N9 ANGL. DEV. = 3.3 DEGREES REMARK 500 DC B 13 C4' - C3' - C2' ANGL. DEV. = -4.2 DEGREES REMARK 500 DC B 13 O4' - C1' - N1 ANGL. DEV. = 3.4 DEGREES REMARK 500 DG B 14 OP1 - P - OP2 ANGL. DEV. = -9.6 DEGREES REMARK 500 DG B 14 P - O5' - C5' ANGL. DEV. = -9.7 DEGREES REMARK 500 DC B 13 C3' - O3' - P ANGL. DEV. = 26.0 DEGREES REMARK 500 DA B 15 O5' - C5' - C4' ANGL. DEV. = -8.8 DEGREES REMARK 500 DA B 15 O4' - C1' - N9 ANGL. DEV. = 4.2 DEGREES REMARK 500 DA B 15 C5 - C6 - N1 ANGL. DEV. = -3.2 DEGREES REMARK 500 DG B 16 C1' - O4' - C4' ANGL. DEV. = -6.3 DEGREES REMARK 500 DG B 16 O4' - C1' - N9 ANGL. DEV. = 4.1 DEGREES REMARK 500 DG B 16 C5 - C6 - N1 ANGL. DEV. = 3.1 DEGREES REMARK 500 DA B 15 C3' - O3' - P ANGL. DEV. = 8.0 DEGREES REMARK 500 DA B 17 O5' - C5' - C4' ANGL. DEV. = -5.1 DEGREES REMARK 500 DA B 17 N1 - C2 - N3 ANGL. DEV. = -3.5 DEGREES REMARK 500 DA B 18 OP1 - P - OP2 ANGL. DEV. = -9.5 DEGREES REMARK 500 DA B 18 O5' - P - OP2 ANGL. DEV. = 7.9 DEGREES REMARK 500 DA B 18 C5 - C6 - N1 ANGL. DEV. = -3.1 DEGREES REMARK 500 DT B 19 O5' - C5' - C4' ANGL. DEV. = -5.8 DEGREES REMARK 500 DT B 19 C2 - N3 - C4 ANGL. DEV. = -5.1 DEGREES REMARK 500 DT B 19 N3 - C4 - C5 ANGL. DEV. = 4.1 DEGREES REMARK 500 DT B 20 O4' - C1' - N1 ANGL. DEV. = 3.4 DEGREES REMARK 500 DT B 20 C2 - N3 - C4 ANGL. DEV. = -4.7 DEGREES REMARK 500 DT B 20 N3 - C4 - C5 ANGL. DEV. = 4.5 DEGREES REMARK 500 DC B 21 O5' - C5' - C4' ANGL. DEV. = -8.1 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 54 ANGLE DEVIATIONS. REMARK 500 REMARK 500 REMARK: NULL
DBREF 153D A 1 12 PDB 153D 153D 1 12 DBREF 153D B 13 24 PDB 153D 153D 13 24
SEQRES 1 A 12 DC DG DA DG DA DA DT DT DC 6OG DC DG SEQRES 1 B 12 DC DG DA DG DA DA DT DT DC 6OG DC DG
MODRES 153D 6OG A 10 DG 6-O-METHYL GUANOSINE-5'-MONOPHOSPHATE MODRES 153D 6OG B 22 DG 6-O-METHYL GUANOSINE-5'-MONOPHOSPHATE
HET 6OG A 10 23 HET 6OG B 22 23
HETNAM 6OG 6-O-METHYL GUANOSINE-5'-MONOPHOSPHATE
FORMUL 1 6OG 2(C11 H16 N5 O7 P) FORMUL 3 HOH *49(H2 O)
LINK O3' DC A 9 P 6OG A 10 1555 1555 1.59 LINK O3' 6OG A 10 P DC A 11 1555 1555 1.55 LINK O3' DC B 21 P 6OG B 22 1555 1555 1.58 LINK O3' 6OG B 22 P DC B 23 1555 1555 1.60
CRYST1 25.130 40.450 64.510 90.00 90.00 90.00 P 21 21 21 8
ORIGX1 1.000000 0.000000 0.000000 0.00000
ORIGX2 0.000000 1.000000 0.000000 0.00000
ORIGX3 0.000000 0.000000 1.000000 0.00000
SCALE1 0.039793 0.000000 0.000000 0.00000
SCALE2 0.000000 0.024722 0.000000 0.00000
SCALE3 0.000000 0.000000 0.015501 0.00000